Contacts of the helix formed by residues 334 - 339 (chain A) in PDB entry 1XV9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ASP* 3.1 45.6 + - + +
333A HIS* 1.3 80.5 - - + +
335A ASN* 1.3 64.2 + - - +
337A ALA* 3.1 9.9 - - - +
338A HIS* 3.0 28.0 - - + +
346A PHE* 3.6 19.7 - - + -
347A ASP* 3.4 29.1 + - - +
350A LEU* 4.5 5.7 - - - +
256C LEU* 3.2 46.8 + - + +
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Residues in contact with ASN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A MET* 4.3 15.4 - - + +
333A HIS* 3.1 29.3 + - + -
334A ARG* 1.3 80.1 - - - +
336A SER* 1.3 56.7 - - - +
337A ALA 2.9 4.9 - - - -
338A HIS* 3.5 5.1 + - - +
339A SER* 3.0 32.6 + - - -
256C LEU* 4.4 17.2 - - - +
339C SER* 4.9 0.5 - - - +
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA* 3.4 8.4 + - - -
253A ASN 3.2 20.9 + - - -
254A MET* 3.1 25.9 - - - +
264A PRO* 3.9 15.2 - - - +
332A VAL* 4.6 6.7 - - - -
333A HIS* 3.4 20.7 + - - +
335A ASN* 1.3 77.8 - - - +
337A ALA* 1.3 59.6 + - - +
339A SER* 3.0 19.3 + - - -
340A ALA* 3.3 14.0 - - - +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PRO* 5.9 0.9 - - - -
332A VAL* 5.3 2.9 - - + -
333A HIS 3.4 1.8 + - - -
334A ARG 3.1 13.9 + - - +
335A ASN 2.9 1.2 - - - -
336A SER* 1.3 75.1 - - - +
338A HIS* 1.3 58.3 + - + +
339A SER 3.1 0.9 - - - -
340A ALA* 2.6 29.0 + - - +
341A GLY 3.2 6.6 + - - -
342A VAL* 3.5 13.9 + - + +
343A GLY* 4.0 8.7 - - - -
346A PHE* 3.4 43.3 - - + -
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Residues in contact with HIS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ARG* 3.0 28.0 + - + +
335A ASN* 4.2 3.8 - - - +
337A ALA* 1.3 79.3 - - + +
339A SER* 1.3 58.0 + - - +
341A GLY* 2.8 21.3 + - - -
343A GLY* 3.7 26.5 - - - +
344A ALA* 4.5 2.0 - - - -
347A ASP* 3.1 35.5 + - - -
254C MET 5.5 0.9 - - - +
255C GLY 3.8 15.0 + - - -
256C LEU* 3.4 43.2 - - + +
258C PRO* 5.6 4.5 - - + -
339C SER* 3.1 14.4 - - - +
340C ALA* 3.4 4.4 - - - +
341C GLY* 3.2 12.1 + - - -
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A MET* 2.8 33.4 + - - +
255A GLY 4.3 5.9 - - - +
256A LEU* 4.8 7.9 - - - +
335A ASN 3.0 15.8 + - - -
336A SER* 3.0 20.0 + - - -
338A HIS* 1.3 76.3 - - - +
340A ALA* 1.3 55.1 + - - +
341A GLY 3.3 0.7 - - - -
338C HIS* 3.2 30.5 - - - +
339C SER* 3.1 7.7 + - - -
341C GLY* 3.4 11.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il